Acellular scaffolds are used for the surgical repair of soft tissue injury forming a biological basis for cell remodelling. Previously tissue-dependent effects sodium-dodecyl-sulphate (SDS) have been determined on the extracellular matrix (ECM) of different tissue types. This short report aims at extending these findings onto a tissue-layer level with focus on the ECM. Porcine ureters, oesophagi and skin underwent acellularisation using SDS, whereas control samples remained in a native condition. The samples were investigated histologically and ultrastructurally electron microscopy. Dense collagen bundles were seen in all native samples throughout the layers, and moderate to strong decreases in collagen density in the acellular state, accompanied by clumping. Collagen bundles were altered differently. Transition from straightened into coiled alignment was observed in the ureters’ intima and all oesophageal layers, the opposite was observed in the ureters’ media and adventitia. Skin samples appeared discontinuously following acellularisation, with collagens curling in the subcutis and dermis and disruptions in the subepidermis. Collagen fibre integrity appeared unchanged. SDS-related alterations include tissue- and site-dependent alterations of the collagen bundles. These insights into the ECM provide further explanation of acellularisation-induced change in mechanical properties, resulting in increased stiffness in ureters, and stiffness in skin. (Folia Morphol 2017; 76, 3: 355–360)